The pygmy rabbit has been present within the semi-arid Columbia Basin shrub-steppe biome in Washington State for over 100,000 years. Little was known about the distribution and status of pygmy rabbits in the state until Washington Department of Fish and Wildlife conducted surveys between 1987 and 1990. Pygmy rabbits were known from six relatively small, isolated populations in Central Washington during the 1990â€™s. Between 1997 and 2001 five of the six populations disappeared and by March 2001 rabbits remained only at Sagebrush Flat Wildlife Area. Large-scale loss and fragmentation of native shrub-steppe habitats likely played a primary role in the long-term decline of the Columbia Basin pygmy rabbit. However, once population numbers dropped below a certain threshold, a combination of other factors such as environmental events (e.g., extreme weather and fire), predation, disease, loss of genetic diversity, and inbreeding likely contributed to the extirpation of populations. WDFW conducted genetic analyses of pygmy rabbits in 2001 and found that the Columbia Basin population appears to have suffered from a reduction in genetic diversity over the past 50 years.

The pygmy rabbit was listed as a threatened species in Washington State in 1990 and was reclassified to endangered status in 1993. A state recovery plan for the rabbit was written in 1995. The U.S. Fish and Wildlife Service listed pygmy rabbits of the Columbia Basin in Washington under emergency provisions of the federal Endangered Species Act in November 2001. A final rule continued the endangered listing in March 2003. Recovery objectives are to increase pygmy rabbit numbers and distribution and manage habitat for long-term protection of features that support pygmy rabbits.

With so few unique Washington pygmy rabbits left in the wild, it was decided to capture 16 of the remaining rabbits in May 2001 to establish a founding captive population for future recovery efforts.

Captive breeding of Columbia Basin pygmy rabbits began in 2002 and eventually included three facilities including Washington State University, Northwest Trek Wildlife Park and Oregon Zoo. A Science Advisory Group, with members from state and federal wildlife agencies, universities, and zoos was formed to review and direct all aspects of captive breeding and population recovery. Unfortunately, from the first breeding season reproductive output was very poor and Columbia Basin pygmy rabbits produced far fewer young than captive Idaho pygmy rabbits in the same facilities. Idaho populations were found to be approximately two-times as diverse as the Columbia Basin population. This lack of genetic diversity in the founder population suggests that inbreeding depression may be linked to the poor reproductive success, skeletal deformities in a few offspring, as well as widespread disease issues in the captive population.

To address the breeding and disease issues in captivity, Columbia Basin and Idaho pygmy rabbits were intercrossed. The resulting offspring exhibited higher fitness in captivity than purebred Columbia Basin pygmy rabbits and purebred offspring produced failed to survive to maturity. Reproduction of purebred Columbia Basin pygmy rabbits ceased due to continuing poor reproductive success and likely reduced fitness of the population. It was decided by the Science Advisory Group that intercross animals with a lower percentage of the foundersâ€™ genes and higher genetic diversity needed to be produced for release. This was expected to result in genetic rescue or genetic restoration by introducing more genetically diverse individuals from another population. Genetic diversity did increase as a result of intercrossing animals, with reproduction largely improving for captive rabbits progressively over the years. Unfortunately, while production of kits increased, the survival of emerged kits decreased, with maternal neglect and disease the most common causes of mortality. Therefore, the number of pygmy rabbits the captive breeding program produced was not sufficient to allow for large-scale reintroductions. In 2011, it was decided that the recovery strategy needed to be adapted in order to succeed.